Dear FreeSurfers,
I am new to Freesurfer and attempting to run a very basic analysis, but am finally stuck after trying 3 alternative ways of displaying the data. Any help would be greatly appreciated!
I have 4 wedges/quadrants (no expanding rings), and want to show areas responding to each ofthe 4 *on an inflated brain*. tksurfer doesn't allow multiple zstats to be presented simultaneously so overlaying the zstats from FSL isn't an option. My next plan was to use a basic block-related design and run contrasts, but mkcontrast-sess produced an error which I have copied below. (Note: I also tried -ncond 4 -a 4 -c 1 -c 2 -c 3)
-------------------------------------------------------- [Main@Brain1]$ mkcontrast-sess -contrast upperright -analysis er.self.lh -ncond 4 -wcond -1 -1 -1 3 INFO: Found 4 Non-Null Conditions INFO: Found 1 Delays Runtime error (func=(main), adr=3): Divide by zero Runtime error (func=(main), adr=4): Divide by zero Condition Weights: -1 -1 -1 3 mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile er.self.lh/upperright.mat nconds 4, wcond -1 -1 -1 3 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave ------------------------------------------------------------------------------
RETINOTOPY ERROR: After the above didn't work, I then started a retinotopic analysis using the steps on the wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis), but as I only have wedges and no rings, in my case I only have 1 run and one rtopy.par file - both under bold/001. However, when I try to view the output using the commard 'tksurfer-sess -a rtopy.self.lh -s L_quads' I get the below error.
------------------------------------------------------------------------------ [Main@Brain1]$ tksurfer-sess -a rtopy.self.lh -s L_V123quads Surface self lh Map Surface self lh $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ Linux Brain1 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux Wed Oct 12 18:02:29 PDT 2011 /usr/local/freesurfer/bin/tksurfer
list eccen polar ERROR: cannot find /usr/local/freesurfer/sessions/Subj001/L_V123quads/bold/rtopy.self.lh/eccen ------------------------------------------------------------------------------
I saw the suggestions on a previous thread about fooling the analysis by copying the polar data into the eccen directory, but I'm still confused - should be creating identical directories (ie. 002, 003, 004) containing the identical dataset but different rtopy.par files? All I have under rtopy.self.lh is an 'analysis.info' file.
Any ideas? At the moment I have no way of displaying my data, and I'm going round in circles, so any suggestions would be great!
Thanks in advance, Jodie
Hi Jodie, I'm still not sure what you are trying to show. If you want to show each wedge separately, then you will need four contrasts of the form "-a 1 -c 0", "-a 2 -c 0", etc. If you want to show places where a voxel responds to *any* of the four, you can use "-a 1 -a 2 -a 3 -a 4 -nosumconds". This will create an F-test (basically an OR of all the conditions). Alternatively, you can run it with "-a 1 -a 2 -a 3 -a 4". This will just add all of them together.
doug
Jodie Davies-Thompson wrote:
Dear FreeSurfers,
I am new to Freesurfer and attempting to run a very basic analysis, but am finally stuck after trying 3 alternative ways of displaying the data. Any help would be greatly appreciated!
I have 4 wedges/quadrants (no expanding rings), and want to show areas responding to each of the 4 *on an inflated brain*. tksurfer doesn't allow multiple zstats to be presented simultaneously so overlaying the zstats from FSL isn't an option. My next plan was to use a basic block-related design and run contrasts, but mkcontrast-sess produced an error which I have copied below. (Note: I also tried -ncond 4 -a 4 -c 1 -c 2 -c 3)
[Main@Brain1]$ mkcontrast-sess -contrast upperright -analysis er.self.lh -ncond 4 -wcond -1 -1 -1 3 INFO: Found 4 Non-Null Conditions INFO: Found 1 Delays Runtime error (func=(main), adr=3): Divide by zero Runtime error (func=(main), adr=4): Divide by zero Condition Weights: -1 -1 -1 3 mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile er.self.lh/upperright.mat nconds 4, wcond -1 -1 -1 3 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave
RETINOTOPY ERROR: After the above didn't work, I then started a retinotopic analysis using the steps on the wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis), but as I only have wedges and no rings, in my case I only have 1 run and one rtopy.par file - both under bold/001. However, when I try to view the output using the commard 'tksurfer-sess -a rtopy.self.lh -s L_quads' I get the below error.
[Main@Brain1]$ tksurfer-sess -a rtopy.self.lh -s L_V123quads Surface self lh Map Surface self lh $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ Linux Brain1 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux Wed Oct 12 18:02:29 PDT 2011 /usr/local/freesurfer/bin/tksurfer
list eccen polar ERROR: cannot find /usr/local/freesurfer/sessions/Subj001/L_V123quads/bold/rtopy.self.lh/eccen
I saw the suggestions on a previous thread about fooling the analysis by copying the polar data into the eccen directory, but I'm still confused - should be creating identical directories (ie. 002, 003, 004) containing the identical dataset but different rtopy.par files? All I have under rtopy.self.lh is an 'analysis.info' file.
Any ideas? At the moment I have no way of displaying my data, and I'm going round in circles, so any suggestions would be great!
Thanks in advance, Jodie
-- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC Canada V5Z 3N9 Tel: 604-875-411 ext 69003
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for your reply. I tried running the contrast you suggested and still get the same error as shown below. I'm guessing it's a problem with my command? What have I done wrong?
Ultimately, I would like to show the response to each wedge as compared to the others. However, I'm hoping to find a way to show all 4 contrasts on the inflated brain together - hence the reason I tried going down the retinotopy route after I couldn't get this working....
Jodie --------------------------------------- [Main@Brain1] $ mkcontrast-sess -contrast upperright -analysis er.self.lh -ncond 4 -a 1 -c 0 INFO: Found 4 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 0 0 0 mkcontrast -anadir er.self.lh -wcond 1.00000000000000000000 0 0 0 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile er.self.lh/upperright.mat nconds 4, wcond 1.00000000000000000000 0 0 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir er.self.lh -wcond 1.00000000000000000000 0 0 0 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -no-octave ---------------------------------------
On 10/13/2011 8:40 AM, Douglas N Greve wrote:
Hi Jodie, I'm still not sure what you are trying to show. If you want to show each wedge separately, then you will need four contrasts of the form "-a 1 -c 0", "-a 2 -c 0", etc. If you want to show places where a voxel responds to *any* of the four, you can use "-a 1 -a 2 -a 3 -a 4 -nosumconds". This will create an F-test (basically an OR of all the conditions). Alternatively, you can run it with "-a 1 -a 2 -a 3 -a 4". This will just add all of them together.
doug
Jodie Davies-Thompson wrote:
Dear FreeSurfers,
I am new to Freesurfer and attempting to run a very basic analysis, but am finally stuck after trying 3 alternative ways of displaying the data. Any help would be greatly appreciated!
I have 4 wedges/quadrants (no expanding rings), and want to show areas responding to each of the 4 *on an inflated brain*. tksurfer doesn't allow multiple zstats to be presented simultaneously so overlaying the zstats from FSL isn't an option. My next plan was to use a basic block-related design and run contrasts, but mkcontrast-sess produced an error which I have copied below. (Note: I also tried -ncond 4 -a 4 -c 1 -c 2 -c 3)
[Main@Brain1]$ mkcontrast-sess -contrast upperright -analysis er.self.lh -ncond 4 -wcond -1 -1 -1 3 INFO: Found 4 Non-Null Conditions INFO: Found 1 Delays Runtime error (func=(main), adr=3): Divide by zero Runtime error (func=(main), adr=4): Divide by zero Condition Weights: -1 -1 -1 3 mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile er.self.lh/upperright.mat nconds 4, wcond -1 -1 -1 3 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave
RETINOTOPY ERROR: After the above didn't work, I then started a retinotopic analysis using the steps on the wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis), but as I only have wedges and no rings, in my case I only have 1 run and one rtopy.par file - both under bold/001. However, when I try to view the output using the commard 'tksurfer-sess -a rtopy.self.lh -s L_quads' I get the below error.
[Main@Brain1]$ tksurfer-sess -a rtopy.self.lh -s L_V123quads Surface self lh Map Surface self lh $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ Linux Brain1 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux Wed Oct 12 18:02:29 PDT 2011 /usr/local/freesurfer/bin/tksurfer
list eccen polar ERROR: cannot find /usr/local/freesurfer/sessions/Subj001/L_V123quads/bold/rtopy.self.lh/eccen
I saw the suggestions on a previous thread about fooling the analysis by copying the polar data into the eccen directory, but I'm still confused - should be creating identical directories (ie. 002, 003, 004) containing the identical dataset but different rtopy.par files? All I have under rtopy.self.lh is an 'analysis.info' file.
Any ideas? At the moment I have no way of displaying my data, and I'm going round in circles, so any suggestions would be great!
Thanks in advance, Jodie
-- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology& Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC Canada V5Z 3N9 Tel: 604-875-411 ext 69003
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
do you have matlab installed? What is the result of the "getmatlab" command?
Jodie Davies-Thompson wrote:
Hi Doug,
Thanks for your reply. I tried running the contrast you suggested and still get the same error as shown below. I'm guessing it's a problem with my command? What have I done wrong?
Ultimately, I would like to show the response to each wedge as compared to the others. However, I'm hoping to find a way to show all 4 contrasts on the inflated brain together - hence the reason I tried going down the retinotopy route after I couldn't get this working....
Jodie
[Main@Brain1] $ mkcontrast-sess -contrast upperright -analysis er.self.lh -ncond 4 -a 1 -c 0 INFO: Found 4 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 0 0 0 mkcontrast -anadir er.self.lh -wcond 1.00000000000000000000 0 0 0 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile er.self.lh/upperright.mat nconds 4, wcond 1.00000000000000000000 0 0 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir er.self.lh -wcond 1.00000000000000000000 0 0 0
-sumconds -o er.self.lh/upperright.mat -wdelay 1 -no-octave
On 10/13/2011 8:40 AM, Douglas N Greve wrote:
Hi Jodie, I'm still not sure what you are trying to show. If you want to show each wedge separately, then you will need four contrasts of the form "-a 1 -c 0", "-a 2 -c 0", etc. If you want to show places where a voxel responds to *any* of the four, you can use "-a 1 -a 2 -a 3 -a 4 -nosumconds". This will create an F-test (basically an OR of all the conditions). Alternatively, you can run it with "-a 1 -a 2 -a 3 -a 4". This will just add all of them together.
doug
Jodie Davies-Thompson wrote:
Dear FreeSurfers,
I am new to Freesurfer and attempting to run a very basic analysis, but am finally stuck after trying 3 alternative ways of displaying the data. Any help would be greatly appreciated!
I have 4 wedges/quadrants (no expanding rings), and want to show areas responding to each of the 4 *on an inflated brain*. tksurfer doesn't allow multiple zstats to be presented simultaneously so overlaying the zstats from FSL isn't an option. My next plan was to use a basic block-related design and run contrasts, but mkcontrast-sess produced an error which I have copied below. (Note: I also tried -ncond 4 -a 4 -c 1 -c 2 -c 3)
[Main@Brain1]$ mkcontrast-sess -contrast upperright -analysis er.self.lh -ncond 4 -wcond -1 -1 -1 3 INFO: Found 4 Non-Null Conditions INFO: Found 1 Delays Runtime error (func=(main), adr=3): Divide by zero Runtime error (func=(main), adr=4): Divide by zero Condition Weights: -1 -1 -1 3 mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile er.self.lh/upperright.mat nconds 4, wcond -1 -1 -1 3 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave
RETINOTOPY ERROR: After the above didn't work, I then started a retinotopic analysis using the steps on the wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis), but as I only have wedges and no rings, in my case I only have 1 run and one rtopy.par file - both under bold/001. However, when I try to view the output using the commard 'tksurfer-sess -a rtopy.self.lh -s L_quads' I get the below error.
[Main@Brain1]$ tksurfer-sess -a rtopy.self.lh -s L_V123quads Surface self lh Map Surface self lh $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ Linux Brain1 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux Wed Oct 12 18:02:29 PDT 2011 /usr/local/freesurfer/bin/tksurfer
list eccen polar ERROR: cannot find /usr/local/freesurfer/sessions/Subj001/L_V123quads/bold/rtopy.self.lh/eccen
I saw the suggestions on a previous thread about fooling the analysis by copying the polar data into the eccen directory, but I'm still confused - should be creating identical directories (ie. 002, 003, 004) containing the identical dataset but different rtopy.par files? All I have under rtopy.self.lh is an 'analysis.info' file.
Any ideas? At the moment I have no way of displaying my data, and I'm going round in circles, so any suggestions would be great!
Thanks in advance, Jodie
-- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC Canada V5Z 3N9 Tel: 604-875-411 ext 69003
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC Canada V5Z 3N9 Tel: 604-875-411 ext 69003
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Jodie Davies-Thompson